Costa-Rica-1-redo-SW
PSP 10022
DNA Source: SporeWorks
General Information
- Accession Date
- May 11, 2021
- Report Type
- Whole-Genome Sequencing
- DNA Source Website
- sporeworks.com
Assessing…
Clone Test
Is Costa-Rica-1-redo-SW a resequencing of a culture already in Psilocydia? Every assembled genome was aligned directly to its closest genome in the collection and the divergence measured. Pairs that are one culture sequenced twice sit at or below about 0.03%; genuinely different cultures sit well above it. Where Costa-Rica-1-redo-SW falls on that scale answers the question, calibrated against the collection's own resequencings rather than a rule of thumb.
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Genetic Information
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What is in the assembly
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Variants
Changes in the psilocybin genes were found by two independent analysis methods applied to this sample's sequencing reads: aligning the reads to the reference genome, and assembling the genome from them. Each change is labelled with the method that found it, or Both; hover a label for the read counts.
How we found these
- Both
- In the assembly and in the reads, so confirmed twice.
- Reads only
- In the reads, not in the assembly. The hover says why where we know: the assembly has the reference base there, does not cover the site, or this sample has no assembly. Many of these are changes carried by only part of the reads; an assembly keeps one base at each position.
- Assembly only
- In the assembly, but the reads show the reference base there, or too few reads cover the site to say.
Read counts. At every site we count the reads carrying each base (reads with mapping quality of at least 20, bases with quality of at least 13; 8 reads or more to say anything). The change is in most reads at 80% or more, mixed between 20% and 80%, in a minority from 5% to 20% (and at least 2 reads), and essentially absent below that. These counts say what the reads show; they say nothing about how many copies of the gene the sample carries. A change counts as found in the reads when these counts show it (in most, mixed or a minority of reads) or when the lab's variant report lists it. That report lists only changes its gene models rate HIGH or MODERATE, so many changes the reads show are not on it.
Names. Protein changes are named on our curated gene models for the psilocybin cluster. The read-alignment report names them on the public reference's gene models, which in places differ (for example, the public models join psiT1 and psiK into one gene); where the names differ, the hover shows both.
What is listed. Changes that alter the protein (rated HIGH or MODERATE), and every change on the lab's variant report for the cluster. Positions are on chromosome 10 of the reference genome.
Genetic Relatives
Nearest
- Costa-Rica-3-redo-SW (PSP10024) — 0.134
- Costa-Rica-2-redo-SW (PSP10023) — 0.140
- Costa-Rica-1-redo-SW (PSP10003) — 0.226
- Costa-Rica-2-redo-SW (PSP10004) — 0.239
- Penvy-Col5-PS (PSP10044) — 0.270
- Penvy-1-PS (PSP10045) — 0.270
- Penvy-2-SW (PSP10075) — 0.271
- Penvy-Col4-PS (PSP10043) — 0.271
- Roatan-Honduras-4-Mush (PSP10079) — 0.323
- Treasure-coast-1-PS (PSP10054) — 0.328
- Treasure-coast-3-PS (PSP10056) — 0.328
- Treasure-coast-2-PS (PSP10055) — 0.328
- Treasure-Coast-2-Mush (PSP10082) — 0.328
- ColumbiaRust-1-SW (PSP10021) — 0.331
- Orissa-India-4-Mush (PSP10073) — 0.331
- Arenal-Volcano-1-Mush (PSP10059) — 0.332
- Bplus-ITW-WM (PSP10129) — 0.332
- Luminous-lucies-2-PS (PSP10032) — 0.336
- Luminous-lucies-3-PS (PSP10033) — 0.337
- Luminous-lucies-1-PS (PSP10034) — 0.337
Most Distant
- Bplus-3-PS (PSP10001) — 0.669
- GoldenCoast-BAF-B1-UM (PSP10107) — 0.668
- Maui-2-PS (PSP10041) — 0.668
- Huautla-3-PS (PSP10005) — 0.667
- GoldenCoast-BAF-B2-UM (PSP10108) — 0.667
- Huautla-3-redo-SW (PSP10031) — 0.667
- GoldenCoast-BAF-A1-UM (PSP10105) — 0.666
- Bplus-2-redo-SW (PSP10015) — 0.666
- Huautla-2-redo-SW (PSP10030) — 0.666
- Bplus-1-redo-SW (PSP10014) — 0.666
- Bplus-3-redo-SW (PSP10016) — 0.666
- Maui-3-PS (PSP10042) — 0.665
- GoldenTeacher-3-SW (PSP10029) — 0.665
- Puerto-Rican-ITW (PSP10078) — 0.665
- Maui-1-PS (PSP10040) — 0.665
- Ecuador-3-SW (PSP10025) — 0.665
- Orissa-India-ITW (PSP10071) — 0.665
- GoldenCoast-BAF-A2-UM (PSP10106) — 0.665
- Golden-Teacher (PSP10089) — 0.662
- GoldenTeacher-1-SW (PSP10027) — 0.662
Sequence Data Downloads
The blockchain-registered VCF above can be downloaded by anyone, so its hash can be checked independently against the blockchain record. The remaining sequence data files — FASTQ, BAM and assemblies — are available to authorised accounts. Log in to download, or contact us for access.
Psilocybin
The psilocybin biosynthesis genes sit together in one cluster on chromosome 10 (psiD, psiK, psiM, psiH, psiR, psiT1, psiT2). Every assembled genome in Psilocydia was compared with the MGC_Penvy_1 reference across this window; below are the variants Costa-Rica-1-redo-SW carries there, and which other samples carry the same ones. This section compares assemblies only; the psilocybin gene cards under Variants combine the assembly with the reads, so they can list changes that are not here.
Costa-Rica-1-redo-SW is not yet in the psilocybin cluster comparison: its assembly did not meet the completeness threshold used to build it, or it has not been assembled. The comparison is refreshed with each pipeline run.
See the psilocybin cluster across the whole collection →Blockchain Registration Information
- Transaction ID
-
c23961a1d9c4c394
67d4f2e7600528ca 4283dd75c1014e6c 3d775e94af734c04 - Stamping Certificate
- Download PDF (39.6 KB)
- SHASUM Hash
-
c97d9754aeff2793a86a7421ac16f16d 2a801071f524fb4c 5500550949a6e1ab